[Psidev-pi-dev] New version 3.86.0 of psi-ms.obo

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Dear proteomics community,

attached there's the new version 3.86.0 of the psi-ms.obo file.
It contains all changes agreed on at the HUPO-PSI meeting in Ghent.

New CV terms in version 3.86.0 of psi-ms.obo:
=================================================
************ added 11 terms for identifier formats for combined spectra
[Term]
id: MS:1002646
name: native spectrum identifier format, combined spectra
def: "Describes how the native spectrum identifiers that have been 
combined prior to searching or interpretation are formated." [PSI:PI]
synonym: "nativeID format, combined spectra" EXACT []
relationship: part_of MS:1000577 ! raw data file

[Term]
id: MS:1002647
name: Thermo nativeID format, combined spectra
def: "Thermo comma separated list of spectra that have been combined 
prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002648
name: Waters nativeID format, combined spectra
def: "Waters comma separated list of spectra that have been combined 
prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002649
name: WIFF nativeID format, combined spectra
def: "WIFF comma separated list of spectra that have been combined prior 
to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002650
name: Bruker/Agilent YEP nativeID format, combined spectra
def: "Bruker/Agilent comma separated list of spectra that have been 
combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002651
name: Bruker BAF nativeID format, combined spectra
def: "Bruker BAF comma separated list of spectra that have been combined 
prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002652
name: Bruker FID nativeID format, combined spectra
def: "Bruker FID comma separated list of spectra that have been combined 
prior to searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002653
name: multiple peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to 
searching or interpretation." [PSI:PI]
comment: Used for conversion of peak list files with multiple spectra, 
i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the 
file, starting from 0.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002654
name: single peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to 
searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID. Used for 
conversion of peak list files with one spectrum per file, typically 
folder of PKL or DTAs, each sourceFileRef is different.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002655
name: scan number only nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to 
searching or interpretation." [PSI:PI]
comment: Used for conversion from mzXML, or DTA folder where native scan 
numbers can be derived.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002656
name: spectrum identifier nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to 
searching or interpretation." [PSI:PI]
comment: Used for conversion from mzData. The spectrum id attribute is 
referenced.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002657
name: mzML unique identifier, combined spectra
def: "Comma separated list of spectra that have been combined prior to 
searching or interpretation." [PSI:PI]
comment: A unique identifier of a spectrum stored in an mzML file.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002658
name: identification parameter
def: "Identification parameter for the search engine run." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

Changed CV terms in version 3.86.0 of psi-ms.obo:
=================================================
************ Added is_a: MS:1002489 ! special processing
[Term]
id: MS:1001010
name: de novo search
def: "A de novo sequencing search (without database)." [PSI:PI]
is_a: MS:1001080 ! search type
is_a: MS:1002489 ! special processing

************ New parent MS:1002657 ! identification parameter
[Term]
id: MS:1002496
name: group PSMs by sequence
def: "Group PSMs by distinct peptide sequence ignoring modifications." 
[PSI:PI]
is_a: MS:1002658 ! identification parameter

[Term]
id: MS:1002497
name: group PSMs by sequence with modifications
def: "Group PSMs by distinct peptide sequence with taking modifications 
into account." [PSI:PI]
is_a: MS:1002658 ! identification parameter

[Term]
id: MS:1002498
name: group PSMs by sequence with modifications and charge
def: "Group PSMs by distinct peptide sequence with taking modifications 
and charge into account." [PSI:PI]
is_a: MS:1002658 ! identification parameter

************ Obsoleted the term 'peptide level score'
[Term]
id: MS:1002499
name: peptide level score
def: "OBSOLETE Peptide level score." [PSI:PI]
comment: This term was obsoleted because it was never intended to go in 
the CV.
is_a: MS:1002358 ! search engine specific score for distinct peptides
is_obsolete: true

************ Changed the definition
[Term]
id: MS:1002643
name: peptide start positions on chromosome
def: "A comma separated list of start positions within exons to which 
the peptide has been mapped, relative to peptide-chromosome start, 
assuming a zero-based counting system. The first value MUST match the 
value in peptide start on chromosome." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

************ Added is_a: MS:1001184 ! search statistics
[Term]
id: MS:1002404
name: count of identified proteins
def: "The number of proteins that have been identified, which must match 
the number of groups that pass the threshold in the file." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein result details
is_a: MS:1001184 ! search statistics

************ Removed the value and unit from the following terms:
[Term]
id: MS:1000904
name: product ion m/z delta
def: "The difference in m/z of the predicted m/z based on the assigned 
product ion minus the actual observed peak m/z." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of a single product ion." [PSI:PI]
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1002225
name: average product ion intensity
def: "Average value of product ion intensity in a collection of 
identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity

[Term]
id: MS:1002226
name: product ion intensity standard deviation
def: "Standard deviation of product ion intensity in a collection of 
identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity

Best Regards,
Gerhard

-- 

*--*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>